Is Pope Francis I's past enough to damn him?

Pope Francis flourished, occupying a prominent position in the Argentine church, at a time when its leaders worked hand in glove with one of the most brutal dictatorships of the 20th century. Is that enough to damn him?

When Jorge Mario Bergoglio stepped onto the Vatican balcony as the new pope Francis yesterday evening, the world was instantly charmed by his gentle, unassuming manner and moved by anecdotes about his love of, and identification with, the poor. To many the first Latin American and the first Jesuit to become Pope looks like a breath of fresh air. While almost as old as Pope Benedict was when he was elected, he seems more approachable and down to earth than his austerely professorial predecessor; and while his views on sexual morality are as conservative as one might expect, he also looks set to prioritise questions of social justice over ones of ecclesiastical discipline. Even name Francis seems to point to a new humility – already his watchword – in the Catholoic Church.

But not everyone has given the new pontiff an unreserved welcome. In Argentina he is a divisive figure, not just because of his outspoken views on subjects such as gay marriage but, more pointedly, because of continuing questions over his and the church's role during the dark years of the late 1970s.

It was a time when a military dictatorship responsible for the abduction, torture and murder of many thousands of its own citizens looked to the Catholic Church for moral legitimacy. A time when the murderous General Jorge Videla cultivated a pious image and claimed to be restoring "Christian morals and values" to the nation, and when – according to the late Christopher Hitchens – the papal nuncio was a regular tennis partner of Admiral Emilio Massero, the regime's torturer in chief.

Finally brought to justice thirty years later, an unrepentent Videla described his trial as "one more act of service to the Lord our Father and to the country."

"It's appalling," the anthropologist Laura Agustín told me yesterday on hearing the news of Bergoglio's elevation. "Seeing his face takes me right back to a nightmare."

The case against Bergoglio is both general and particular. As leader of the church in Argentina since 1997, he stands accused of reluctance to properly face up to Catholic complicity with the regime. He twice invoked legal privilege to avoid testifying in cases resulting from the "Dirty War" of the 1970s. When he finally did give evidence in 2010, some observers found his testimony evasive and less than helpful. It wasn't until late last year that Argentina's bishops issued a collective apology in for the church's past failure to stand up to the dictatorship, and even then failed to satisfy critics. The statement acknowledged the role of some senior clerics in supporting the military junta, but fell short of accepting institutional responsibility for the church and had harsh words for Catholics who supported violent resistance to the dictatorship.

Such a belated and tentative acknowledgement of wrongdoing smacks rather of the "too little, too late" approach that has cost the Catholic Church credibility in its response to other scandals of recent years, notably the sexual abuse of children by priests. It hardly suggests that the new pope will be in a hurry to tackle the church's problems head on.

Bergoglio's eventual mea culpa went nowhere near as far as a statement offered by another priest at the 2007 trial of Fr Christian von Wernich, a former prison chaplain who was convicted of direct complicity in seven murders, 42 abductions and 31 cases of torture. On that occasion, Rubén Capitanio told the court that the church had been "scandalously close to the dictatorship. . . to a sinful degree." The church was "like a mother that did not look out for her children," he went on. "It did not kill anybody, but it did not save anybody either."

Argentina was not unique in Latin America for coming under military rule during the 1970s, but the role played by the Catholic church in supporting the regime was unusual. As in Spain under Franco, patriotism and Catholicism came to be closely linked in Argentina. There are even suggestions that bishops gave their blessing to General Jorge Videla and his fellow generals prior to the military coup of March 24th 1976. It's a matter of record that on the day of the coup, the then Archbishop of Buenos Aires Adolfo Tortolo emerged from a meeting with the junta to urge his fellow citizens to cooperate "in a positive way" with the new government. He later went out of his way to deny that any human rights abuses were being committed in Argentina.

How much did senior clerics actually know about what was going on? According to the investigative journalist Horacio Verbitsky, who is among the new pope's leading critics, declassified documents reveal that a meeting of bishops in May 1976 heard chilling details of persecution, arbitrary arrest and even torture, but nevertheless voted by a majority to issue a statement calling for understanding towards the military government. The bishops even justified human rights abuses by the regime, stating that "it was wrong to insist that the security agencies act "with the chemical purity of peacetime, while blood runs every day."

As leader of the Jesuit order in Argentina at the time of the coup, Jorge Bergoglio was in a tricky position. He never publicly supported the regime. Speaking out against it, meanwhile, would have carried real dangers: several priests, and two bishops, were among the victims of the Dirty War. But he is accused of more than simply keeping his head down while others sacrificed theirs. The most serious allegation, which formed the basis of a formal criminal complaint in 2005, is that he knew about and failed to prevent the abduction and torture of two fellow Jesuit priests.

The priests, Orlando Yokio and Francisco Jalics, had come under suspicion for their work in the Bajo Flores slum district and for their association with a group of activists that included Monica Mignone, daughter of a prominent lawyer, all of whom later disappeared into the regime's dungeons. The two Jesuits' work, and the liberation theology that inspired it, also attracted the critical attention of their superiors in the church, notably Bergoglio himself, who reportedly offered them a choice between leaving the slum or leaving their priestly ministry. Their licence to minister was withdrawn by the then archbishop a week before they were seized.

According to Verbitsky, whose book The Silence detailed the relationship between church and state in that dark period, the military took the church's action as a green light to have them arrested. What is undoubtedly the case is that there was a certain community of interest between the anti-communism of the military regime and the Church hierarchy's dislike of liberation theology.

Both men were released in October 1976 after five months of interrogation and torture in the notorious Navy Mechanics School, ESMA (where Fr Wernach served as chaplain). In The Jesuit, a collection of conversations between Bergoglia and the writer Sergio Rubin, it is claimed that, far from denouncing Yorio and Jalics, Bergoglio warned the two priests of the danger they were in and later intervened behind the scenes to secure their release. But this is contested. Verbitsky quotes Yorio (who died in 2000) as telling him explicitly that "Bergoglio failed to warn us of danger waiting to happen" and that "I have no reason to think he did something for our freedom, but rather the opposite".

Verbitsky also spoke to Monica Mignone's mother Angelica, who asserted that the two priests "were freed by the efforts of Emilio Mignone and the intercession of the Vatican, not by the actions of Bergoglio, who betrayed them". Another of his interviewees, Yorio's brother Rodolfo, described Bergoglio as "a politician who loves power." Much the same comment, seemingly at odds with the new Pope's modest demeanour, was made last night on Argentine radio by Eduardo de la Serna, coordinator of a left-wing group of priests, who described him as "a man of power [who] knows how position himself among powerful people."

The 2005 complaint did not, in the end, lead to charges being laid against Cardinal Bergoglio, and the truth may never be known. He has strenuously denied any wrongdoing, and has dismissed the allegations as "old slander." That Yurio and Jalics believed that Bergoglio had betrayed them does not of course mean that he did, nor were they in a position to know what private action Bergoglio might have taken on their behalf.

In some ways, the controversy surrounding the new pope recalls that over Pope Pius XII, accused by his critics of not speaking out against the Nazis, while his defenders counter that he did what he could behind the scenes to help individual victims. Bergolgio's own faults may have amounted to little more than naivety and holiness: the very humility that was so widely and instantly acclaimed when he stepped onto the Vatican balcony last night. Perhaps the most damning thing that can be said about him is that he survived, and flourished, occupying a prominent position in the Argentine church at a time when its leaders worked hand in glove with one of the most brutal dictatorships of the 20th century.